install_github fails is a release note for every release

[revodavid]

Several users report that install_github is failing on Ubuntu 14.04:
https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/rropen/GeCyC-wfWA4/r9lvM2s8uRMJ

> library(devtools)
> devtools::install_github("twitter/BreakoutDetection")
Downloading github repo twitter/BreakoutDetection@master
Error in system(full, intern = quiet, ignore.stderr = quiet, ...) : 
  error in running command

As a workaround, install_git appears to work:

> devtools::install_github("smbache/magrittr", ref = "dev")
Downloading github repo smbache/magrittr@dev
Error in system(full, intern = quiet, ignore.stderr = quiet, ...) : 
  error in running command
> devtools::install_git("git://github.com/smbache/magrittr.git", branch = "dev")

[revodavid]

It seemed possible that this was a bug in the 2014-10-1 version of devtools on the MRAN snapshot, but it worked fine for me on MacOS:

> install.packages("devtools")
also installing the dependencies ‘bitops’, ‘httr’, ‘RCurl’, ‘memoise’, ‘whisker’, ‘rstudioapi’, ‘jsonlite’

[snip]

> install_github("twitter/BreakoutDetection")
Downloading github repo twitter/BreakoutDetection@master
Installing BreakoutDetection
Installing dependencies for BreakoutDetection:
Rcpp, ggplot2, Rcpp
also installing the dependencies ‘colorspace’, ‘dichromat’, ‘munsell’, ‘labeling’, ‘plyr’, ‘gtable’, ‘reshape2’, ‘scales’, ‘proto’

[snip]

* installing *source* package ‘BreakoutDetection’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DPLATFORM_PKGTYPE='"mac.binary.mavericks"' -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o

[snip]
** testing if installed package can be loaded
* DONE (BreakoutDetection)

[cmosetick]

@revodavid I confirm that this issue is still present on Ubuntu 14.04. I tested inside a fresh RRO Ubuntu docker container.

devtools::install_github("twitter/BreakoutDetection") does not work.
Only this command worked:
devtools::install_git("git://github.com/smbache/magrittr.git", branch = "dev")

I then tested this on the last RRO Ubuntu 14.04 build artifact from 8.0.1 beta from November 13th and it still does not work.

I tested this on RRO for Mac as well. I made sure that I was using the 2014-10-01 snapshot and
devtools::install_github("twitter/BreakoutDetection")
worked fine for me there.

[revodavid]

Please retest in 8.0.1-beta3

[sfweller]

This is still a problem in 8.0.1 beta3. It looks to me like the problem is due to differences in how the system() command is invoked on Ubuntu systems. Will look at this issue more closely to verify exactly where the problem is.

[sfweller]

I have determined what the source of the problem is - the issue has been reported here on Hadley's github website:
r-lib/devtools#406

The problem is that on Ubuntu systems, you get the following:

getOption("unzip")
[1] " "

whereas 'install_github()' expects:

getOption('unzip')
[1] "internal"

A quick fix for customers is to simply set:
options(unzip = 'internal')

After doing this it works.

Do we want to doc this or add this to our notes?

[dkarlov]

This problem also occurred on suse 12.2

[revodavid]

@dkarlov, can you tell us what the result of getOption("unzip") is on your system? Setting options(unzip="internal") should work around the problem, but I am unsure whether RRO is behaving differently to R in this regard,

[dkarlov]

getOption("unzip")
[1] ""

[dkarlov]

install_git worked perfectly

[revodavid]

A call do install_git of this form also works around the issue:

devtools::install_git("https://github.com/ramnathv/htmlwidgets.git", branch = "master")

[revodavid]

It was included in the release notes for 3.2.0 and should be included in release notes for future versions until the issue is resolved.

[j-martens]

In every release, add the following to the release notes:

Known Issues

• devtools::install_github may fail with the error "error in running command" on Ubuntu and openSUSE. To work around this issue, set options(unzip = 'internal') before calling install_github. (See install_github fails is a release note for every release #37 and 'unzip' must be a single character string when calling install_github r-lib/devtools#406 )

[j-martens]

Doc'ed here: https://github.com/RA-Internal/MRAN-site/issues/197

[mtelesha]

Just wanted to also state like dkarlov reported on March 12 that OpenSUSE has an issue. I am using OpenSUSE 13.2 and it failed.

options(unzip = 'internal') did fix it for OpenSUSE 13.2

[j-martens]

Thank you, @mtelesha
We'll make note of it in the release notes.

[aaronthor]

Hi, just wanted to report that:

require(devtools)
install_github('ramnathv/rCharts')
Downloading github repo ramnathv/rCharts@master
Error in system(full, intern = quiet, ignore.stderr = quiet, ...) :
error in running command

still doesn't work in Ubuntu 14.04 X64..
Although:

install_git('https://github.com/ramnathv/rCharts.git')

works, it leads to issues when uploading to shinyapps.io with the following errors:

   Preparing to deploy application...DONE
   Uploading bundle for application: 61854...Error: 
   * Unable to deploy package dependency 'rCharts'
    The package was installed locally from source. Only packages
    installed from CRAN, BioConductor and GitHub are supported.
  Execution halted 

Thanks

[sfweller]

Hi Aaron,

This is a known issue and we should document this in our release.
To workaround the issue, you can do the following in R, BEFORE calling install_github():

options(unzip = 'internal')

Hope this helps.

Stephen Weller
Revolution R Open Technical Support

[aaronthor]

Hello Stephen,

Appreciate your response with the workaround. Unfortunately, I had to drop
out of my Coursera course as I wasn't able to submit my final project..
Will try with the workaround when I get home this evening. Thank you.

Have a marvelous day ahead Stephen!

Cheers,
Aaron

On Tue, Sep 29, 2015 at 6:07 AM, Stephen Weller notifications@github.com
wrote:

Hi Aaron,

This is a known issue and we should document this in our release.
To workaround the issue, you can do the following in R, BEFORE calling
install_github():

options(unzip = 'internal')

Hope this helps.

Stephen Weller
Revolution R Open Technical Support

—
Reply to this email directly or view it on GitHub
#37 (comment)
.

[j-martens]

Hello!

As you may now know, this is a known devtools issue (not an RRO issue). The workaround Stephen mentioned is documented earlier in this thread and is part of the release notes for the last 3 releases of RRO; however, it might not be easy to find the answer.

Have a good day,
Josée

[aaronthor]

Hello Josée and Stephen,

Yeah, I've missed it somehow. Got it working now. Appreciate your guidance fellas!
Have a wonderful weekend ahead!

Cheers,
Aaron

[tshtatland]

Thank you for documenting the workaround. I am adding:

Known Issues

• devtools::install_bitbucket() may fail with the error "error in running command" on Ubuntu. To work around this issue, set options(unzip = 'internal') before calling install_bitbucket.

Example:

> library(devtools)
> install_bitbucket("repo_name")
Downloading bitbucket repo repo_name
Installation failed: error in running command
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] devtools_1.13.2

loaded via a namespace (and not attached):
[1] httr_1.2.1    R6_2.2.2      withr_1.0.2   curl_2.8.1    memoise_1.1.0
[6] git2r_0.19.0  digest_0.6.12

[seonghobae]

another solution in ubuntu 16.04: run apt install unzip